Starting phenix.real_space_refine on Wed Aug 5 21:24:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1s_42889/08_2026/8v1s_42889_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1s_42889/08_2026/8v1s_42889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v1s_42889/08_2026/8v1s_42889_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1s_42889/08_2026/8v1s_42889_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v1s_42889/08_2026/8v1s_42889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1s_42889/08_2026/8v1s_42889.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 59 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7398 2.51 5 N 2106 2.21 5 O 2277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11889 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8602 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1091, 8582 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1091, 8582 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 3 bond proxies already assigned to first conformer: 8759 Chain: "B" Number of atoms: 2079 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2070 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 14, 'TRANS': 254} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2070 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 14, 'TRANS': 254} Chain breaks: 1 bond proxies already assigned to first conformer: 2098 Chain: "P" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 536 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "T" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 671 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 700 " occ=0.44 ... (20 atoms not shown) pdb=" NH2BARG A 700 " occ=0.56 residue: pdb=" N ALYS A1182 " occ=0.52 ... (16 atoms not shown) pdb=" NZ BLYS A1182 " occ=0.48 residue: pdb=" N ALYS B 105 " occ=0.43 ... (16 atoms not shown) pdb=" NZ BLYS B 105 " occ=0.57 Time building chain proxies: 3.42, per 1000 atoms: 0.29 Number of scatterers: 11889 At special positions: 0 Unit cell: (154.275, 115.5, 89.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 59 15.00 Mg 1 11.99 O 2277 8.00 N 2106 7.00 C 7398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 747.6 milliseconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 38.7% alpha, 19.1% beta 12 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 168 through 175 removed outlier: 4.399A pdb=" N MET A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.702A pdb=" N ARG A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.611A pdb=" N PHE A 335 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.621A pdb=" N LEU A 350 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 430 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.705A pdb=" N ASP A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 559 through 567 removed outlier: 4.186A pdb=" N GLY A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 593 Processing helix chain 'A' and resid 593 through 606 removed outlier: 3.789A pdb=" N GLU A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 617 through 632 removed outlier: 4.293A pdb=" N VAL A 621 " --> pdb=" O GLN A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.843A pdb=" N ASP A 703 " --> pdb=" O AARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 772 through 790 Processing helix chain 'A' and resid 796 through 816 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 830 through 855 Processing helix chain 'A' and resid 858 through 866 Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 901 through 917 removed outlier: 3.790A pdb=" N LYS A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 980 Processing helix chain 'A' and resid 983 through 990 Processing helix chain 'A' and resid 996 through 1001 removed outlier: 4.268A pdb=" N ALA A1000 " --> pdb=" O GLU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1007 through 1023 removed outlier: 3.755A pdb=" N VAL A1013 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1059 Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1145 through 1152 removed outlier: 3.646A pdb=" N HIS A1152 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1174 removed outlier: 3.872A pdb=" N TYR A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1178 removed outlier: 3.559A pdb=" N GLY A1178 " --> pdb=" O ALA A1175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1175 through 1178' Processing helix chain 'A' and resid 1180 through 1189 Processing helix chain 'A' and resid 1190 through 1192 No H-bonds generated for 'chain 'A' and resid 1190 through 1192' Processing helix chain 'A' and resid 1199 through 1209 removed outlier: 4.487A pdb=" N ARG A1205 " --> pdb=" O ASP A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1235 removed outlier: 3.735A pdb=" N THR A1223 " --> pdb=" O THR A1219 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A1224 " --> pdb=" O ALA A1220 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A1225 " --> pdb=" O GLU A1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.614A pdb=" N ALYS B 105 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 4.003A pdb=" N ARG B 113 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 273 through 281 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 removed outlier: 9.046A pdb=" N VAL A 436 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 409 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU A 438 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 411 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 440 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER A 413 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 406 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP A 400 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 392 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL A 391 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS A 372 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 113 removed outlier: 9.046A pdb=" N VAL A 436 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 409 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU A 438 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 411 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 440 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER A 413 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 406 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP A 400 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 392 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 156 Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 208 Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 Processing sheet with id=AA9, first strand: chain 'A' and resid 708 through 709 removed outlier: 3.821A pdb=" N LYS A 928 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR A 884 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU A 893 " --> pdb=" O ILE A 882 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 882 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 709 removed outlier: 6.580A pdb=" N VAL A 944 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 933 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 942 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 754 through 755 Processing sheet with id=AB3, first strand: chain 'A' and resid 1212 through 1215 Processing sheet with id=AB4, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.879A pdb=" N TRP B 141 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 123 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B 139 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU B 125 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 137 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE B 127 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR B 135 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.879A pdb=" N TRP B 141 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 123 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B 139 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU B 125 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 137 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE B 127 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR B 135 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.598A pdb=" N GLN B 76 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 255 through 257 removed outlier: 8.485A pdb=" N VAL B 256 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 222 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 200 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 265 " --> pdb=" O LEU B 204 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.07: 1 1.07 - 1.27: 1789 1.27 - 1.46: 5232 1.46 - 1.66: 5179 1.66 - 1.86: 73 Bond restraints: 12274 Sorted by residual: bond pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 1.473 1.863 -0.390 1.40e-02 5.10e+03 7.77e+02 bond pdb=" CG PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 1.503 0.867 0.636 3.40e-02 8.65e+02 3.50e+02 bond pdb=" C1' DT P -12 " pdb=" N1 DT P -12 " ideal model delta sigma weight residual 1.468 1.565 -0.097 1.40e-02 5.10e+03 4.85e+01 bond pdb=" C3' DG T 21 " pdb=" O3' DG T 21 " ideal model delta sigma weight residual 1.435 1.519 -0.084 1.30e-02 5.92e+03 4.22e+01 bond pdb=" CB ASN A 518 " pdb=" CG ASN A 518 " ideal model delta sigma weight residual 1.516 1.364 0.152 2.50e-02 1.60e+03 3.70e+01 ... (remaining 12269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 16893 14.77 - 29.54: 3 29.54 - 44.30: 1 44.30 - 59.07: 0 59.07 - 73.84: 1 Bond angle restraints: 16898 Sorted by residual: angle pdb=" CB PRO B 132 " pdb=" CG PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 106.10 179.94 -73.84 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO B 132 " pdb=" CD PRO B 132 " pdb=" CG PRO B 132 " ideal model delta sigma weight residual 103.20 72.74 30.46 1.50e+00 4.44e-01 4.12e+02 angle pdb=" CA PRO B 132 " pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 112.00 86.76 25.24 1.40e+00 5.10e-01 3.25e+02 angle pdb=" CA PRO B 132 " pdb=" CB PRO B 132 " pdb=" CG PRO B 132 " ideal model delta sigma weight residual 104.50 77.70 26.80 1.90e+00 2.77e-01 1.99e+02 angle pdb=" N PRO B 132 " pdb=" CA PRO B 132 " pdb=" C PRO B 132 " ideal model delta sigma weight residual 113.86 124.08 -10.22 1.25e+00 6.40e-01 6.68e+01 ... (remaining 16893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 6616 34.54 - 69.07: 531 69.07 - 103.61: 26 103.61 - 138.15: 1 138.15 - 172.68: 6 Dihedral angle restraints: 7180 sinusoidal: 3240 harmonic: 3940 Sorted by residual: dihedral pdb=" CA ALA A 220 " pdb=" C ALA A 220 " pdb=" N PRO A 221 " pdb=" CA PRO A 221 " ideal model delta harmonic sigma weight residual 180.00 -123.91 -56.09 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA GLY B 305 " pdb=" C GLY B 305 " pdb=" N PRO B 306 " pdb=" CA PRO B 306 " ideal model delta harmonic sigma weight residual -180.00 -125.50 -54.50 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA SER A1038 " pdb=" C SER A1038 " pdb=" N ARG A1039 " pdb=" CA ARG A1039 " ideal model delta harmonic sigma weight residual -180.00 -126.53 -53.47 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 7177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1144 0.062 - 0.125: 534 0.125 - 0.187: 176 0.187 - 0.249: 39 0.249 - 0.311: 12 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CB VAL B 212 " pdb=" CA VAL B 212 " pdb=" CG1 VAL B 212 " pdb=" CG2 VAL B 212 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB VAL A 253 " pdb=" CA VAL A 253 " pdb=" CG1 VAL A 253 " pdb=" CG2 VAL A 253 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASP B 146 " pdb=" N ASP B 146 " pdb=" C ASP B 146 " pdb=" CB ASP B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1902 not shown) Planarity restraints: 1975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 131 " 0.180 5.00e-02 4.00e+02 2.15e-01 7.42e+01 pdb=" N PRO B 132 " -0.368 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " 0.098 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 48 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO B 49 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 716 " -0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C PHE A 716 " 0.080 2.00e-02 2.50e+03 pdb=" O PHE A 716 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP A 717 " -0.027 2.00e-02 2.50e+03 ... (remaining 1972 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 88 2.45 - 3.06: 8441 3.06 - 3.68: 19079 3.68 - 4.29: 27983 4.29 - 4.90: 46522 Nonbonded interactions: 102113 Sorted by model distance: nonbonded pdb=" O LEU A 583 " pdb=" OE1 GLN A 587 " model vdw 1.841 3.040 nonbonded pdb=" OG1 THR A 312 " pdb=" O ALA A 602 " model vdw 1.933 3.040 nonbonded pdb=" OD2 ASP A 471 " pdb="MG MG A1301 " model vdw 1.970 2.170 nonbonded pdb=" OD1 ASP A 471 " pdb="MG MG A1301 " model vdw 1.973 2.170 nonbonded pdb=" OG SER A 127 " pdb=" O LEU A 129 " model vdw 1.974 3.040 ... (remaining 102108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.320 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.636 12274 Z= 0.881 Angle : 1.659 73.840 16898 Z= 0.960 Chirality : 0.081 0.311 1905 Planarity : 0.015 0.215 1975 Dihedral : 22.660 172.682 4648 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.55 % Rotamer: Outliers : 0.18 % Allowed : 31.32 % Favored : 68.50 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.93 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.48 (0.19), residues: 1357 helix: -2.28 (0.20), residues: 440 sheet: -2.69 (0.31), residues: 224 loop : -3.62 (0.19), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 302 TYR 0.034 0.005 TYR A 490 PHE 0.043 0.005 PHE A 733 TRP 0.024 0.005 TRP A 502 HIS 0.025 0.004 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.01843 / 0.88 (12274) covalent geometry : angle 1.65906 / 0.96 (16898) hydrogen bonds : bond 0.16013 / 11.00 ( 489) hydrogen bonds : angle 8.26753 / 5.93 ( 1363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 281 TYR cc_start: 0.6443 (t80) cc_final: 0.6147 (t80) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1026 time to fit residues: 15.9250 Evaluate side-chains 100 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.171307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.147304 restraints weight = 55014.465| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 4.75 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12274 Z= 0.248 Angle : 0.971 17.858 16898 Z= 0.521 Chirality : 0.058 0.314 1905 Planarity : 0.008 0.087 1975 Dihedral : 22.871 175.574 2150 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.10 % Rotamer: Outliers : 3.64 % Allowed : 27.51 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.21), residues: 1357 helix: -1.25 (0.22), residues: 447 sheet: -2.35 (0.32), residues: 222 loop : -2.63 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 214 TYR 0.022 0.003 TYR A1148 PHE 0.036 0.003 PHE B 98 TRP 0.025 0.003 TRP A 781 HIS 0.008 0.002 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.25 (12274) covalent geometry : angle 0.97055 / 0.52 (16898) hydrogen bonds : bond 0.06516 / 4.38 ( 489) hydrogen bonds : angle 6.55797 / 4.78 ( 1363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7602 (mmm) cc_final: 0.7214 (mmm) REVERT: A 481 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7167 (p0) REVERT: A 615 ASP cc_start: 0.8040 (p0) cc_final: 0.7836 (p0) REVERT: A 756 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.5517 (mt-10) outliers start: 39 outliers final: 17 residues processed: 157 average time/residue: 0.1080 time to fit residues: 24.2174 Evaluate side-chains 124 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.0670 chunk 59 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.171064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.147409 restraints weight = 52251.279| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 4.53 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12274 Z= 0.233 Angle : 0.872 10.629 16898 Z= 0.465 Chirality : 0.056 0.388 1905 Planarity : 0.007 0.068 1975 Dihedral : 22.756 178.966 2150 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.45 % Favored : 93.40 % Rotamer: Outliers : 3.64 % Allowed : 27.68 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.21), residues: 1357 helix: -0.84 (0.22), residues: 450 sheet: -1.95 (0.32), residues: 217 loop : -2.41 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 558 TYR 0.035 0.003 TYR A 557 PHE 0.024 0.003 PHE B 98 TRP 0.019 0.002 TRP A 502 HIS 0.007 0.002 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (12274) covalent geometry : angle 0.87238 / 0.47 (16898) hydrogen bonds : bond 0.05948 / 4.01 ( 489) hydrogen bonds : angle 6.08230 / 4.41 ( 1363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 427 LEU cc_start: 0.7605 (mp) cc_final: 0.7292 (mt) REVERT: A 451 MET cc_start: 0.7856 (mmm) cc_final: 0.7385 (mmm) REVERT: A 510 GLN cc_start: 0.5863 (OUTLIER) cc_final: 0.4588 (mt0) REVERT: A 615 ASP cc_start: 0.8030 (p0) cc_final: 0.7795 (p0) REVERT: A 756 GLU cc_start: 0.5817 (OUTLIER) cc_final: 0.5382 (mt-10) REVERT: A 950 MET cc_start: 0.7045 (tpp) cc_final: 0.6592 (tpp) REVERT: B 51 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7847 (mtt-85) outliers start: 39 outliers final: 26 residues processed: 158 average time/residue: 0.0965 time to fit residues: 22.2815 Evaluate side-chains 137 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 134 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 247 HIS A 806 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.172801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.148178 restraints weight = 54297.050| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 4.73 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12274 Z= 0.188 Angle : 0.810 10.196 16898 Z= 0.431 Chirality : 0.054 0.320 1905 Planarity : 0.006 0.069 1975 Dihedral : 22.653 179.844 2150 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 4.44 % Allowed : 27.68 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.22), residues: 1357 helix: -0.52 (0.23), residues: 459 sheet: -1.74 (0.31), residues: 233 loop : -2.05 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 214 TYR 0.028 0.002 TYR A 67 PHE 0.034 0.002 PHE A 313 TRP 0.017 0.002 TRP A 781 HIS 0.006 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (12274) covalent geometry : angle 0.81040 / 0.43 (16898) hydrogen bonds : bond 0.05228 / 3.53 ( 489) hydrogen bonds : angle 5.71040 / 4.12 ( 1363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.283 Fit side-chains REVERT: A 427 LEU cc_start: 0.7703 (mp) cc_final: 0.7347 (mt) REVERT: A 451 MET cc_start: 0.7749 (mmm) cc_final: 0.7325 (mmm) REVERT: A 510 GLN cc_start: 0.5483 (OUTLIER) cc_final: 0.4408 (mt0) REVERT: A 756 GLU cc_start: 0.5706 (OUTLIER) cc_final: 0.5230 (mt-10) REVERT: A 950 MET cc_start: 0.7113 (tpp) cc_final: 0.6696 (tpp) REVERT: B 51 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7483 (mtt-85) REVERT: B 309 VAL cc_start: 0.6166 (OUTLIER) cc_final: 0.5190 (p) outliers start: 48 outliers final: 32 residues processed: 163 average time/residue: 0.0904 time to fit residues: 21.4672 Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 136 optimal weight: 30.0000 chunk 133 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 323 ASN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.171656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.147668 restraints weight = 42045.545| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 3.47 r_work: 0.3722 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12274 Z= 0.217 Angle : 0.810 10.423 16898 Z= 0.429 Chirality : 0.053 0.302 1905 Planarity : 0.006 0.071 1975 Dihedral : 22.610 176.646 2150 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 5.32 % Allowed : 26.71 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.22), residues: 1357 helix: -0.44 (0.23), residues: 457 sheet: -1.52 (0.32), residues: 230 loop : -1.97 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 222 TYR 0.020 0.002 TYR A 316 PHE 0.020 0.003 PHE B 98 TRP 0.010 0.001 TRP A 856 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (12274) covalent geometry : angle 0.81032 / 0.43 (16898) hydrogen bonds : bond 0.05277 / 3.57 ( 489) hydrogen bonds : angle 5.68930 / 4.10 ( 1363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 119 time to evaluate : 0.265 Fit side-chains REVERT: A 427 LEU cc_start: 0.7797 (mp) cc_final: 0.7204 (mt) REVERT: A 451 MET cc_start: 0.7700 (mmm) cc_final: 0.7362 (mmm) REVERT: A 510 GLN cc_start: 0.5183 (OUTLIER) cc_final: 0.4158 (mt0) REVERT: A 515 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 756 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.5162 (mt-10) REVERT: A 934 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6884 (tp) REVERT: A 950 MET cc_start: 0.7255 (tpp) cc_final: 0.6923 (tpp) REVERT: A 1054 VAL cc_start: 0.6258 (OUTLIER) cc_final: 0.5822 (m) REVERT: B 51 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7712 (mtt-85) REVERT: B 309 VAL cc_start: 0.6938 (OUTLIER) cc_final: 0.6006 (p) outliers start: 58 outliers final: 39 residues processed: 163 average time/residue: 0.0844 time to fit residues: 20.3536 Evaluate side-chains 155 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 6.9990 chunk 138 optimal weight: 40.0000 chunk 128 optimal weight: 9.9990 chunk 31 optimal weight: 0.4980 chunk 85 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A1157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.175114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.152308 restraints weight = 46078.034| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 4.01 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12274 Z= 0.163 Angle : 0.767 9.555 16898 Z= 0.405 Chirality : 0.051 0.307 1905 Planarity : 0.006 0.070 1975 Dihedral : 22.358 171.802 2150 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.97 % Favored : 92.95 % Rotamer: Outliers : 4.08 % Allowed : 27.86 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.22), residues: 1357 helix: -0.23 (0.24), residues: 462 sheet: -1.44 (0.31), residues: 227 loop : -1.86 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 90 TYR 0.018 0.002 TYR A1148 PHE 0.022 0.002 PHE A 965 TRP 0.017 0.002 TRP A 781 HIS 0.014 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (12274) covalent geometry : angle 0.76727 / 0.41 (16898) hydrogen bonds : bond 0.04814 / 3.23 ( 489) hydrogen bonds : angle 5.45058 / 3.92 ( 1363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.403 Fit side-chains REVERT: A 99 LEU cc_start: 0.5028 (mp) cc_final: 0.4752 (tp) REVERT: A 365 MET cc_start: 0.7341 (ttp) cc_final: 0.7113 (ttp) REVERT: A 451 MET cc_start: 0.7866 (mmm) cc_final: 0.7450 (mmm) REVERT: A 510 GLN cc_start: 0.5230 (OUTLIER) cc_final: 0.4390 (mt0) REVERT: A 756 GLU cc_start: 0.5620 (OUTLIER) cc_final: 0.5161 (mt-10) REVERT: A 981 ASP cc_start: 0.5359 (m-30) cc_final: 0.5100 (p0) REVERT: A 999 LEU cc_start: 0.7601 (mt) cc_final: 0.7041 (mt) REVERT: A 1054 VAL cc_start: 0.6000 (OUTLIER) cc_final: 0.5660 (m) REVERT: B 51 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7610 (mtt-85) REVERT: B 309 VAL cc_start: 0.5947 (OUTLIER) cc_final: 0.5233 (p) outliers start: 44 outliers final: 28 residues processed: 168 average time/residue: 0.0909 time to fit residues: 22.3012 Evaluate side-chains 148 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.172711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149096 restraints weight = 63189.182| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 5.22 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12274 Z= 0.202 Angle : 0.778 10.025 16898 Z= 0.409 Chirality : 0.051 0.304 1905 Planarity : 0.007 0.133 1975 Dihedral : 22.324 173.046 2150 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 4.26 % Allowed : 27.95 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.22), residues: 1357 helix: -0.19 (0.24), residues: 458 sheet: -1.31 (0.31), residues: 230 loop : -1.81 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 222 TYR 0.021 0.002 TYR A 399 PHE 0.019 0.002 PHE A 965 TRP 0.009 0.001 TRP A 856 HIS 0.004 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (12274) covalent geometry : angle 0.77763 / 0.41 (16898) hydrogen bonds : bond 0.04916 / 3.34 ( 489) hydrogen bonds : angle 5.50398 / 3.95 ( 1363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.434 Fit side-chains REVERT: A 348 ASP cc_start: 0.6788 (p0) cc_final: 0.6577 (p0) REVERT: A 451 MET cc_start: 0.7897 (mmm) cc_final: 0.7494 (mmm) REVERT: A 510 GLN cc_start: 0.5350 (OUTLIER) cc_final: 0.4650 (mt0) REVERT: A 756 GLU cc_start: 0.5598 (OUTLIER) cc_final: 0.5086 (mt-10) REVERT: A 934 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6710 (tp) REVERT: A 981 ASP cc_start: 0.5670 (m-30) cc_final: 0.5306 (p0) REVERT: A 1054 VAL cc_start: 0.6043 (OUTLIER) cc_final: 0.5732 (m) REVERT: B 51 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7739 (mtt-85) REVERT: B 309 VAL cc_start: 0.6096 (OUTLIER) cc_final: 0.5426 (p) outliers start: 46 outliers final: 36 residues processed: 158 average time/residue: 0.1182 time to fit residues: 27.0990 Evaluate side-chains 163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.178060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.155468 restraints weight = 51370.298| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 3.93 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4105 r_free = 0.4105 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4105 r_free = 0.4105 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12274 Z= 0.156 Angle : 0.753 10.521 16898 Z= 0.395 Chirality : 0.049 0.309 1905 Planarity : 0.006 0.095 1975 Dihedral : 22.165 171.985 2150 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 4.08 % Allowed : 28.13 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.22), residues: 1357 helix: -0.07 (0.24), residues: 461 sheet: -1.27 (0.31), residues: 228 loop : -1.74 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 222 TYR 0.018 0.002 TYR A 818 PHE 0.019 0.002 PHE A 965 TRP 0.014 0.002 TRP A 781 HIS 0.004 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (12274) covalent geometry : angle 0.75311 / 0.39 (16898) hydrogen bonds : bond 0.04632 / 3.13 ( 489) hydrogen bonds : angle 5.37963 / 3.84 ( 1363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.400 Fit side-chains REVERT: A 365 MET cc_start: 0.7363 (ttp) cc_final: 0.7150 (ttp) REVERT: A 451 MET cc_start: 0.7708 (mmm) cc_final: 0.7374 (mmm) REVERT: A 510 GLN cc_start: 0.5117 (OUTLIER) cc_final: 0.4772 (mt0) REVERT: A 756 GLU cc_start: 0.5598 (OUTLIER) cc_final: 0.5117 (mt-10) REVERT: A 999 LEU cc_start: 0.7407 (mt) cc_final: 0.6858 (mt) REVERT: B 51 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7402 (mtt-85) REVERT: B 309 VAL cc_start: 0.5978 (OUTLIER) cc_final: 0.5079 (p) outliers start: 44 outliers final: 35 residues processed: 162 average time/residue: 0.1148 time to fit residues: 26.6271 Evaluate side-chains 157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 94 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 127 optimal weight: 0.0470 chunk 64 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 912 HIS A1152 HIS A1157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.178779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.156531 restraints weight = 53209.885| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 4.04 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4115 r_free = 0.4115 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4115 r_free = 0.4115 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12274 Z= 0.155 Angle : 0.747 9.449 16898 Z= 0.392 Chirality : 0.049 0.306 1905 Planarity : 0.006 0.085 1975 Dihedral : 22.046 172.697 2150 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 3.99 % Allowed : 28.84 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.23), residues: 1357 helix: 0.05 (0.24), residues: 460 sheet: -1.24 (0.32), residues: 227 loop : -1.68 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 90 TYR 0.019 0.002 TYR A 259 PHE 0.025 0.002 PHE A 965 TRP 0.012 0.001 TRP A 856 HIS 0.004 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (12274) covalent geometry : angle 0.74664 / 0.39 (16898) hydrogen bonds : bond 0.04491 / 3.03 ( 489) hydrogen bonds : angle 5.32937 / 3.81 ( 1363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.390 Fit side-chains REVERT: A 451 MET cc_start: 0.7762 (mmm) cc_final: 0.7404 (mmm) REVERT: A 510 GLN cc_start: 0.4955 (OUTLIER) cc_final: 0.4700 (mt0) REVERT: A 756 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.5104 (mt-10) REVERT: A 1019 ARG cc_start: 0.6437 (ttp80) cc_final: 0.6232 (tmm160) REVERT: A 1086 THR cc_start: 0.7564 (p) cc_final: 0.7323 (t) REVERT: B 51 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7550 (mtt-85) REVERT: B 309 VAL cc_start: 0.5983 (OUTLIER) cc_final: 0.5170 (p) outliers start: 43 outliers final: 37 residues processed: 158 average time/residue: 0.1149 time to fit residues: 26.4115 Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 19 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 729 HIS A 912 HIS A1157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.177373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.154743 restraints weight = 41571.785| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.32 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12274 Z= 0.185 Angle : 0.758 9.679 16898 Z= 0.398 Chirality : 0.050 0.307 1905 Planarity : 0.006 0.062 1975 Dihedral : 22.023 173.150 2150 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 3.73 % Allowed : 29.02 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.23), residues: 1357 helix: 0.01 (0.24), residues: 460 sheet: -1.18 (0.32), residues: 230 loop : -1.69 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1019 TYR 0.025 0.002 TYR A 818 PHE 0.024 0.002 PHE A 965 TRP 0.013 0.001 TRP A 856 HIS 0.021 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (12274) covalent geometry : angle 0.75843 / 0.40 (16898) hydrogen bonds : bond 0.04659 / 3.18 ( 489) hydrogen bonds : angle 5.37339 / 3.83 ( 1363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.268 Fit side-chains REVERT: A 451 MET cc_start: 0.7759 (mmm) cc_final: 0.7436 (mmm) REVERT: A 510 GLN cc_start: 0.4981 (OUTLIER) cc_final: 0.4712 (mt0) REVERT: A 560 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7414 (mm) REVERT: A 756 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.5065 (mt-10) REVERT: A 934 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6633 (tp) REVERT: A 1054 VAL cc_start: 0.5869 (OUTLIER) cc_final: 0.5628 (m) REVERT: A 1086 THR cc_start: 0.7558 (p) cc_final: 0.7329 (t) REVERT: B 265 PHE cc_start: 0.5656 (p90) cc_final: 0.5044 (p90) outliers start: 40 outliers final: 34 residues processed: 147 average time/residue: 0.1061 time to fit residues: 22.9259 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 132 optimal weight: 0.0570 chunk 135 optimal weight: 40.0000 chunk 80 optimal weight: 2.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 912 HIS A1157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.178571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.156842 restraints weight = 58520.571| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 4.41 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12274 Z= 0.156 Angle : 0.743 9.226 16898 Z= 0.390 Chirality : 0.050 0.307 1905 Planarity : 0.005 0.062 1975 Dihedral : 21.959 172.692 2150 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.73 % Allowed : 29.02 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.23), residues: 1357 helix: 0.09 (0.24), residues: 459 sheet: -1.18 (0.32), residues: 226 loop : -1.67 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1019 TYR 0.024 0.002 TYR A 818 PHE 0.023 0.002 PHE A 965 TRP 0.014 0.001 TRP A 856 HIS 0.015 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (12274) covalent geometry : angle 0.74266 / 0.39 (16898) hydrogen bonds : bond 0.04526 / 3.08 ( 489) hydrogen bonds : angle 5.34272 / 3.81 ( 1363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2165.67 seconds wall clock time: 38 minutes 5.89 seconds (2285.89 seconds total)